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  <div class="section" id="tools">
<h1>tools<a class="headerlink" href="#tools" title="Permalink to this headline">¶</a></h1>
<div class="section" id="module-atomman.tools">
<span id="functions-and-attributes"></span><h2>Functions and attributes<a class="headerlink" href="#module-atomman.tools" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="atomman.tools.aslist">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">aslist</code><span class="sig-paren">(</span><em class="sig-param">term</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.aslist" title="Permalink to this definition">¶</a></dt>
<dd><p>Create list representation of term. Treats a str, unicode term as a single
item.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>term</strong> (<em>any</em>) – Term to convert into a list, if needed.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>All items in term as a list</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>list of any</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.atomic_mass">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">atomic_mass</code><span class="sig-paren">(</span><em class="sig-param">atomic_info</em>, <em class="sig-param">mass_number=None</em>, <em class="sig-param">prompt=True</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.atomic_mass" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns either the median standard atomic weight for an element or the relative
atomic mass for an isotope.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>atomic_info</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a>) – The atomic symbol or number identifying the element/isotopes.</p></li>
<li><p><strong>mass_number</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – An isotope mass number.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The average standard atomic weight of an element or the relative
atomic mass of an isotope.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)">float</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.atomic_number">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">atomic_number</code><span class="sig-paren">(</span><em class="sig-param">atomic_symbol</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.atomic_number" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the corresponding atomic number for a given atomic symbol.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>atomic_symbol</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – An atomic symbol.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The corresponding atomic number.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)">int</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.atomic_symbol">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">atomic_symbol</code><span class="sig-paren">(</span><em class="sig-param">atomic_number</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.atomic_symbol" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the corresponding atomic symbol for a given atomic number.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>atomic_number</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a>) – An atomic number.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The corresponding atomic symbol.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)">int</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.axes_check">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">axes_check</code><span class="sig-paren">(</span><em class="sig-param">axes</em>, <em class="sig-param">tol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.axes_check" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks that given axes are orthogonal and right-handed.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>axes</strong> (<em>list of list</em><em> or </em><em>np.ndarray</em>) – A 3x3 array of axes vectors.</p></li>
<li><p><strong>tol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Tolerance to use in checking if axes are orthogonal and right-handed.
Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>A 3x3 array of the corresponding unit vectors of axes.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If axes are not orthogonal or right-handed.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.compositionstr">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">compositionstr</code><span class="sig-paren">(</span><em class="sig-param">symbols</em>, <em class="sig-param">counts</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.compositionstr" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a reduced composition string based on symbols and counts.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>symbols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The model symbol for a site.</p></li>
<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – How many sites are occupied by each symbol.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The reduced composition string.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="attribute">
<dt id="atomman.tools.duplicates_allclose">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">duplicates_allclose</code><a class="headerlink" href="#atomman.tools.duplicates_allclose" title="Permalink to this definition">¶</a></dt>
<dd><p>Determine duplicates in dataframe based on tolerances.  The implementation
first uses <cite>pandas.DataFrame.duplicated</cite> on the <cite>dcols</cite> argument with
<cite>keep=False</cite> to keep all duplicates.  The duplicate sub-dataframe is then
sorted on both <cite>dcols</cite> and <cite>fcols</cite>.  A diff between each row is then done
on the sorted duplicates dataframe.  The float values are then checked for
their tolerances.</p>
<p>Note: False duplicates may be identified if tolerance ranges overlap.
Consider dataframe with rows 1,2,3.  If row 2 matches row 1 within the
tolerances, and row 3 matches row 2 within the tolerances, both rows 2 and
3 will be labeled as tolerances even if row 3 does not match row 1 within
the tolerances.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>dataframe</strong> (<em>pandas.DataFrame</em>) – The dataframe to search for duplicates</p></li>
<li><p><strong>dcols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a>) – The column names that are tested for exact duplicates.</p></li>
<li><p><strong>fcols</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a>) – The column names (keys) that are tested using absolute tolerances
(values).</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>False for first occurrence of checked values, True for subsequent
duplicates.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>list of bool of length nrows</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.filltemplate">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">filltemplate</code><span class="sig-paren">(</span><em class="sig-param">template</em>, <em class="sig-param">variable</em>, <em class="sig-param">s_delimiter</em>, <em class="sig-param">e_delimiter</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.filltemplate" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes a template and fills in values for delimited template variables.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>template</strong> (<em>string</em><em> or </em><em>file-like object</em>) – The template file or file content to fill in.</p></li>
<li><p><strong>variable</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.9)"><em>dict</em></a>) – Dictionary with keys defining the delimited template variable terms,
and values the values to replace the variable terms with.</p></li>
<li><p><strong>s_delimiter</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The leading delimiter for identifying the template variable terms.</p></li>
<li><p><strong>e_delimiter</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The trailing delimiter for identifying the template variable terms.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The template with all delimited variable terms replaced with their
corresponding defined values from variable.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#KeyError" title="(in Python v3.9)"><strong>KeyError</strong></a> – If delimited term found in template that has no value in variable.</p></li>
<li><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If parsing of s_delimiter, e_delimiter pairs fails.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.iaslist">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">iaslist</code><span class="sig-paren">(</span><em class="sig-param">term</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.iaslist" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterate over items in term as if term was a list. Treats a str, unicode
term as a single item.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>term</strong> (<em>any</em>) – Term to iterate over.</p>
</dd>
<dt class="field-even">Yields</dt>
<dd class="field-even"><p><em>any</em> – Items in the list representation of term.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.identifyfamily">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">identifyfamily</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.identifyfamily" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard representation
of a crystal system cell.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>‘cubic’, ‘hexagonal’, ‘tetragonal’, ‘rhombohedral’, ‘orthorhombic’,
‘monoclinic’ or ‘triclinic’ if it matches any. None if no matches.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a> or <a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)">None</a></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If box is not consistent with a standard cell.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.indexstr">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">indexstr</code><span class="sig-paren">(</span><em class="sig-param">shape</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.indexstr" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates through all unique indicies of an array with a given shape.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>shape</strong> (<em>tuple of int</em>) – The array shape to iterate through.</p>
</dd>
<dt class="field-even">Yields</dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>index</strong> (<em>tuple of int</em>) – A unique index set of the array.</p></li>
<li><p><strong>istr</strong> (<em>str</em>) – A string representation of index with numbers in [].</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.iscubic">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">iscubic</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.iscubic" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard cubic cell:
a = b = c
alpha = beta = gamma = 90</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard cubic cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.ishexagonal">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">ishexagonal</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.ishexagonal" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard hexagonal cell:
a = b != c
alpha = beta = 90
gamma = 120</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard hexagonal cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.ismonoclinic">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">ismonoclinic</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.ismonoclinic" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard monoclinic cell:
a != b != c
alpha = gamma = 90
beta != 90</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard monoclinic cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.isorthorhombic">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">isorthorhombic</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.isorthorhombic" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard orthorhombic cell:
a != b != c
alpha = beta = gamma = 90</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard orthorhombic cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.isrhombohedral">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">isrhombohedral</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.isrhombohedral" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard rhombohedral cell:
a = b = c
alpha = beta = gamma != 90</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard rhombohedral cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.istetragonal">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">istetragonal</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.istetragonal" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard tetragonal cell:
a = b != c
alpha = beta = gamma = 90</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard tetragonal cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.istriclinic">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">istriclinic</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">rtol=1e-05</em>, <em class="sig-param">atol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.istriclinic" title="Permalink to this definition">¶</a></dt>
<dd><p>Tests if a box is consistent with a standard triclinic cell:
a != b != c
alpha != 90
beta != 90
gamma != 90</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box object to test.</p></li>
<li><p><strong>rtol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Relative tolerance for testing box parameters. Default value is 1e-5.</p></li>
<li><p><strong>atol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Absolute tolerance for testing box parameters. Default value is 1e-8.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>True if box is a standard triclinic cell, False otherwise.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)">bool</a></p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.screen_input">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">screen_input</code><span class="sig-paren">(</span><em class="sig-param">prompt=''</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.screen_input" title="Permalink to this definition">¶</a></dt>
<dd><p>Replacement input function that is compatible with the mingw terminal.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>prompt</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The screen prompt to use for asking for the input.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The user input.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="class">
<dt id="atomman.tools.uber_open_rmode">
<em class="property">class </em><code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">uber_open_rmode</code><span class="sig-paren">(</span><em class="sig-param">data</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.uber_open_rmode" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<p>Context manager for reading data from file-like objects, file names,
and data strings in the same manner.</p>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.vect_angle">
<code class="sig-prename descclassname">atomman.tools.</code><code class="sig-name descname">vect_angle</code><span class="sig-paren">(</span><em class="sig-param">vect1</em>, <em class="sig-param">vect2</em>, <em class="sig-param">unit='degree'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.vect_angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the angle between two vectors.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>vect1</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em> or </em><em>numpy.ndarray</em>) – First vector.</p></li>
<li><p><strong>vect2</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)"><em>list</em></a><em> or </em><em>numpy.ndarray</em>) – Second vector.</p></li>
<li><p><strong>unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – Specifies unit of returned angle: ‘degree’ or ‘radian’. Default value
is ‘degree’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The angle between vect1 and vect2.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)">float</a></p>
</dd>
</dl>
</dd></dl>

<span class="target" id="module-atomman.tools.miller"></span><dl class="function">
<dt id="atomman.tools.miller.plane3to4">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">plane3to4</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.plane3to4" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts 3-term Miller (hkl) plane indices to 4-term hexagonal (hkil)
Miller-Bravias indices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> (<em>np.ndarray</em>) – (…, 3) array of Miller crystallographic indices.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 4) array of Miller-Bravais crystallographic indices.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If indices dimensions are not (…, 3).</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.plane4to3">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">plane4to3</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.plane4to3" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts 4-term hexagonal Miller-Bravias (hkil) plane indices to 3-term
Miller (hkl) indices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> (<em>np.ndarray of int</em>) – (…, 4) array of Miller-Bravais crystallographic indices.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 3) array of Miller crystallographic indices.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray of int</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If indices dimensions are not (…, 4), or if h+k+i != 0.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.vector3to4">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">vector3to4</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.vector3to4" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts 3-term Miller [uvw] vector indices to 4-term hexagonal [uvtw]
Miller-Bravias indices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> (<em>np.ndarray</em>) – (…, 3) array of Miller crystallographic indices.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 4) array of Miller-Bravais crystallographic indices.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If indices dimensions are not (…, 3).</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.vector4to3">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">vector4to3</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.vector4to3" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts 4-term hexagonal Miller-Bravias [uvtw] vector indices to 3-term
Miller [uvw] indices.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> (<em>np.ndarray of int</em>) – (…, 4) array of Miller-Bravais crystallographic indices.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 3) array of Miller crystallographic indices.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray of int</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If indices dimensions are not (…, 4), or if u+v+t != 0.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.plane_crystal_to_cartesian">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">plane_crystal_to_cartesian</code><span class="sig-paren">(</span><em class="sig-param">indices</em>, <em class="sig-param">box</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.plane_crystal_to_cartesian" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts crystal planar indices to Cartesian plane normal vectors relative
to a given lattice box.  Note: the algorithm used requires that the planar
indices be integers.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>indices</strong> (<em>np.ndarray</em>) – (3,) array of [hkl] Miller crystallographic indices or
(4,) array of [hkil] Miller-Bravais crystallographic indices.</p></li>
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – Box that defines the lattice cell vectors to use.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 3) array of Cartesian vectors corresponding to plane normals.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray of float</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If indices dimensions are not (…, 3) or (…, 4), or if
    hexagonal indices given with non-hexagonal box.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.vector_crystal_to_cartesian">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">vector_crystal_to_cartesian</code><span class="sig-paren">(</span><em class="sig-param">indices</em>, <em class="sig-param">box</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.vector_crystal_to_cartesian" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts crystal indices to Cartesian vectors relative
to a given lattice box.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>indices</strong> (<em>np.ndarray</em>) – (…, 3) array of [uvw] Miller crystallographic indices or
(…, 4) array of [uvtw] Miller-Bravais crystallographic indices.</p></li>
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – Box that defines the lattice cell vectors to use.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 3) array of Cartesian vectors.</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray of float</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.9)"><strong>ValueError</strong></a> – If indices dimensions are not (…, 3) or (…, 4), or if
    hexagonal indices given with non-hexagonal box.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.vector_primitive_to_conventional">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">vector_primitive_to_conventional</code><span class="sig-paren">(</span><em class="sig-param">indices</em>, <em class="sig-param">setting='p'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.vector_primitive_to_conventional" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts crystal indices relative to a primitive cell
to indices relative to a conventional cell in a specified setting.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>indices</strong> (<em>np.ndarray</em>) – (…, 3) array of [uvw] Miller crystallographic indices
relative to the primitive cell</p></li>
<li><p><strong>setting</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – Specifies the conventional cell setting: ‘p’ for primitive,
‘a’, ‘b’, ‘c’ for side-centered, ‘i’ for body-centered, and
‘f’ for face-centered.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 3) array of [uvw] Miller crystallographic indices
relative to the conventional cell</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray of float</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><strong>ValuenError</strong> – If indices dimensions are not (…, 3) or if an unknown setting
    value is given.</p>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomman.tools.miller.vector_conventional_to_primitive">
<code class="sig-prename descclassname">atomman.tools.miller.</code><code class="sig-name descname">vector_conventional_to_primitive</code><span class="sig-paren">(</span><em class="sig-param">indices</em>, <em class="sig-param">setting='p'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.tools.miller.vector_conventional_to_primitive" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts crystal indices relative to a conventional cell
in a specified setting to indices relative to a primitive cell.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>indices</strong> (<em>np.ndarray</em>) – (…, 3) array of [uvw] Miller crystallographic indices
relative to the conventional cell</p></li>
<li><p><strong>setting</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – Specifies the conventional cell setting: ‘p’ for primitive,
‘a’, ‘b’, ‘c’ for side-centered, ‘i’ for body-centered, and
‘f’ for face-centered.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>(…, 3) array of [uvw] Miller crystallographic indices
relative to the primitive cell</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p>np.ndarray of float</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><strong>ValuenError</strong> – If indices dimensions are not (…, 3) or if an unknown setting
    value is given.</p>
</dd>
</dl>
</dd></dl>

</div>
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